ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TACTCGCAGTGGAACCTGGTCGCGCAGCACCCCAACTTCGACAACCTCACCACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCAgtgagatcgagcaccaccacctggtcctggacctcgttcgcccccactgaagaaattcaatcttttctttctctttttttttccgcgcgcgtgcag

Basic information

species	Zea mays
transcript	GRMZM2G167520_T02
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G167520_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os07g41310.1 (Oryza sativa), 5'ss of exon 5

TACTCGCAGTGGAACCTGGTCGCGCAGCACCCCAACTTCGACAACCTCACCACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCAgtgagatcgagcaccaccacctggtcctggacctcgttcgcccccactgaagaaattcaatcttttctttctctttttttttccgcgcgcgtgcag
||||| ||||||||||| ||| | ||||||||||  || ||||| || || |||||||||||||||||||||| | || | ||||| || ||||| || ||| ||  |    | ||    ||  || ||    |  ||      ||     || ||| | | |||  ||| ||                       
TACTCTCAGTGGAACCTAGTCACTCAGCACCCCAGTTTTGACAATCTGACAACCATTTTCAGCTTCAACTACAAATCTTTGAACCCATATGGAGTAATAAgtaagccctgaaaacaat-tctactcatgtggttaattatttttca-----gatatttactgtttcttttttcag---------------------

upper sequence: GRMZM2G167520_T02 (Zea mays), 5'ss of exon 6
lower sequence: AT3G29810.1 (Arabidopsis thaliana), 5'ss of exon 5

TACTCGCAGTGGAACCTGGTCGCGCAGCACCCCAACTTCGACAACCTCACCACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCAgtgagatcgagcaccaccacctggtcctggacctcgttcgcccccactgaagaaattcaatcttttctttctctttttttttccgcgcgcgtgcag-
||||| ||||||||| | ||||  ||||| |||||||||||||| ||||| |   ||||||| |||||||||| ||| || || || |||      || ||| || |             ||  | | |   ||   ||     |     | |  ||   | | |  |       | ||||    |     |  |  
TACTCTCAGTGGAACTTAGTCGTTCAGCATCCCAACTTCGACAATCTCACTAAGCTTTTCAGTTTCAACTACAAACCGCTTAATCCTTACTTGAACATAAgtaagttt------------ctcattcagattctttctcttgttcttaagaaatgtttggtttctaataatataatgttttggatcatatattgaag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments

ATGC    EST sequence
ATGC    genomic sequence (exon)
ATGC    genomic sequence (truncated intron)

EST: gi|149106094|gb|EE291758.2|EE291758

EST:     TCAACTACAGACCTCTCAACCCCTACGGAGTGATCA                         ACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGA
genomic: TCAACTACAGACCTCTCAACCCCTACGGAGTGATCAgtgagatcga ... gcgcgtgcagACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGA

EST: gi|71758586|gb|DR956523.1|DR956523

EST:     CACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCA                         ACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGA
genomic: CACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCAgtgagatcga ... gcgcgtgcagACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGA

EST: gi|148942554|gb|EC887573.2|EC887573

EST:     CACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCA                         ACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGA
genomic: CACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCAgtgagatcga ... gcgcgtgcagACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGA

EST: gi|76291094|gb|DV030662.1|DV030662

EST:     CACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCA                         ACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGA
genomic: CACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCAgtgagatcga ... gcgcgtgcagACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGA

EST: gi|71763546|gb|DR961483.1|DR961483

EST:     CACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCA                         ACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGA
genomic: CACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCAgtgagatcga ... gcgcgtgcagACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGA

EST: gi|71767449|gb|DR965386.1|DR965386

EST:     CACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCA                         ACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATTTGCTCATGA
genomic: CACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCAgtgagatcga ... gcgcgtgcagACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGA

EST: gi|71765854|gb|DR963791.1|DR963791

EST:     CACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCA                         ACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGA
genomic: CACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCAgtgagatcga ... gcgcgtgcagACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGA

EST: gi|89759713|gb|DY688444.1|DY688444

EST:     CACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCA                         ACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGA
genomic: CACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCAgtgagatcga ... gcgcgtgcagACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGA

EST: gi|93282999|gb|EB675263.1|EB675263

EST:     CACCATTTTCAGCTTCAACTACAGACCTCTCAACCCTTACGGAGTGATCA                         ACGACACGGCGATGCTATGGGGCATCAAGTATTACAACGATCTGTTCATGA
genomic: CACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCAgtgagatcga ... gcgcgtgcagACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGA

EST: gi|91052459|gb|EB162877.1|EB162877

EST:     CACCATTTTCAGTTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCA                         ACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGA
genomic: CACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCAgtgagatcga ... gcgcgtgcagACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGA

EST: gi|88747178|gb|DY531319.1|DY531319

EST:     CACCATTTTCAGTTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCA                         ACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGA
genomic: CACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCAgtgagatcga ... gcgcgtgcagACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGA

EST: gi|149105204|gb|EE290690.2|EE290690

EST:     CACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCA                         ACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGA
genomic: CACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCAgtgagatcga ... gcgcgtgcagACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGA

EST: gi|149099275|gb|EE185309.2|EE185309

EST:     CACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCA                         ACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGA
genomic: CACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCAgtgagatcga ... gcgcgtgcagACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGA

EST: gi|101399158|gb|EB821453.1|EB821453

EST:     CACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCA                         ACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGA
genomic: CACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCAgtgagatcga ... gcgcgtgcagACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGA

RNA-Seq data

ATGC Supported by RNA-Seq exonic block that spans over the splice site

atgs Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.

Found data for 3 RNA-Seq libraries.

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 27

TACTCGCAGTGGAACCTGGTCGCGCAGCACCCCAACTTCGACAACCTCACCACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCAgtgagatcga ... gcgcgtgcagACGACACGGCGATGCTATGGGGCATCAAGTACTACAACGATCTGCTCATGACGGCCGGGCCAGACGGGAACGTGCAGTCCGAGCTTCTGTTCCGGAAGGA

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 47

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 170

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACTCGCAGTGGAACCTGGTCGCGCAGCACCCCAACTTCGACAACCTCACCACCATTTTCAGCTTCAACTACAGACCTCTCAACCCCTACGGAGTGATCAgtgagatcgagcaccaccacctggtcctggacctcgttcgcccccactgaagaaattcaatcttttctttctctttttttttccgcgcgcgtgcag

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